The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome.

Praveen P, Jordan F, Priami C, Morine MJ - Microbiome (2015)

Bottom Line:
This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities.Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed.

Background: The human intestinal microbiota changes from being sparsely populated and variable to possessing a mature, adult-like stable microbiome during the first 2 years of life. This assembly process of the microbiota can lead to either negative or positive effects on health, depending on the colonization sequence and diet. An integrative study on the diet, the microbiota, and genomic activity at the transcriptomic level may give an insight into the role of diet in shaping the human/microbiome relationship. This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.

Results: We re-analyzed a published metagenomics and host gene expression dataset from a systems biology perspective. Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities. The diversity of the microbiota is higher in formula-fed than breast-fed infants, potentially reflecting the weaker dependence of infants on maternal microbiome. We mapped the microbial composition and the expression patterns for host systems and studied their relationship from a systems biology perspective, focusing on the differences.

Conclusions: Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed. Applying network-based systems biology approach via enrichment of microbial species with host genes revealed the novel key relationships of the microbiota with immune and metabolic activity. This was supported statistically by data and literature.

Fig1: The LEfSe plot for clades of the microbiota under breast-fed (BF) and formula-fed (FF) conditions. The cladograms report the taxa (highlighted by small circles and by shading) showing different abundance values (according to LEfSe). Colors of circle and shading indicate the microbial lineages that are enriched within corresponding samples. LEfSe highlights several genus-level clades, e.g., the class Bacilli is under-abundant in BF samples with an otherwise over-abundant Lactobacillus lineage (indicated with a red shade over green for indices m and n (see adjacent legend)). A contrary example can be seen in case of Enterobacter (indexed as a8)

Mentions:
The microbiota under two feeding conditions showed enrichments with different bacterial lineages (Fig. 1). The microbiota in both feeding conditions had higher fraction of anaerobes compared to facultative anaerobes. The analysis of bacterial phyla in the sample shared high agreement with the findings of Schwartz et al. [14] with the Actinobacteria showing prominence under both feeding conditions (see Additional file 1). The Firmicutes associated with energy resorption and obesity [26] were more abundant in FF samples than in BF samples (see Additional file 1). We also computed the diversity of the microbiota (see Additional file 1) in terms of Shannon index [27].Fig. 1

Fig1: The LEfSe plot for clades of the microbiota under breast-fed (BF) and formula-fed (FF) conditions. The cladograms report the taxa (highlighted by small circles and by shading) showing different abundance values (according to LEfSe). Colors of circle and shading indicate the microbial lineages that are enriched within corresponding samples. LEfSe highlights several genus-level clades, e.g., the class Bacilli is under-abundant in BF samples with an otherwise over-abundant Lactobacillus lineage (indicated with a red shade over green for indices m and n (see adjacent legend)). A contrary example can be seen in case of Enterobacter (indexed as a8)

Mentions:
The microbiota under two feeding conditions showed enrichments with different bacterial lineages (Fig. 1). The microbiota in both feeding conditions had higher fraction of anaerobes compared to facultative anaerobes. The analysis of bacterial phyla in the sample shared high agreement with the findings of Schwartz et al. [14] with the Actinobacteria showing prominence under both feeding conditions (see Additional file 1). The Firmicutes associated with energy resorption and obesity [26] were more abundant in FF samples than in BF samples (see Additional file 1). We also computed the diversity of the microbiota (see Additional file 1) in terms of Shannon index [27].Fig. 1

Bottom Line:
This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities.Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed.

Background: The human intestinal microbiota changes from being sparsely populated and variable to possessing a mature, adult-like stable microbiome during the first 2 years of life. This assembly process of the microbiota can lead to either negative or positive effects on health, depending on the colonization sequence and diet. An integrative study on the diet, the microbiota, and genomic activity at the transcriptomic level may give an insight into the role of diet in shaping the human/microbiome relationship. This study aims at better understanding the effects of microbial community and feeding mode (breast-fed and formula-fed) on the immune system, by comparing intestinal metagenomic and transcriptomic data from breast-fed and formula-fed babies.

Results: We re-analyzed a published metagenomics and host gene expression dataset from a systems biology perspective. Our results show that breast-fed samples co-express genes associated with immunological, metabolic, and biosynthetic activities. The diversity of the microbiota is higher in formula-fed than breast-fed infants, potentially reflecting the weaker dependence of infants on maternal microbiome. We mapped the microbial composition and the expression patterns for host systems and studied their relationship from a systems biology perspective, focusing on the differences.

Conclusions: Our findings revealed that there is co-expression of more genes in breast-fed samples but lower microbial diversity compared to formula-fed. Applying network-based systems biology approach via enrichment of microbial species with host genes revealed the novel key relationships of the microbiota with immune and metabolic activity. This was supported statistically by data and literature.